# Bio.Align.Applications package

## Module contents

Alignment command line tool wrappers (OBSOLETE).

We have decided to remove this module in future, and instead recommend building your command and invoking it via the subprocess module directly.

class Bio.Align.Applications.MuscleCommandline(cmd=default_muscle, **kwargs)

  Bases: `AbstractCommandline`

  Command line wrapper for the multiple alignment program MUSCLE.

  http://www.drive5.com/muscle/

  Notes

  Last checked against version: 3.7, briefly against 3.8

  References

  Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.

  Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113.

  Examples

      >>> from Bio.Align.Applications import MuscleCommandline
      >>> muscle_exe = r"C:\Program Files\Alignments\muscle3.8.31_i86win32.exe"
      >>> in_file = r"C:\My Documents\unaligned.fasta"
      >>> out_file = r"C:\My Documents\aligned.fasta"
      >>> muscle_cline = MuscleCommandline(muscle_exe, input=in_file, out=out_file)
      >>> print(muscle_cline)
      "C:\Program Files\Alignments\muscle3.8.31_i86win32.exe" -in "C:\My Documents\unaligned.fasta" -out "C:\My Documents\aligned.fasta"

  You would typically run the command line with muscle_cline() or via the Python subprocess module, as described in the Biopython tutorial.

  __init__(cmd=default_muscle, **kwargs)

    Initialize the class.

  __firstlineno__ = 23
  __static_attributes__ = ('parameters',)
  property anchors

    Use anchor optimisation in tree dependent refinement iterations

    This property controls the addition of the -anchors switch, treat this property as a boolean.

  property anchorspacing

    Minimum spacing between anchor columns

    This controls the addition of the -anchorspacing parameter and its associated value. Set this property to the argument value required.

  property brenner

    Use Steve Brenner’s root alignment method

    This property controls the addition of the -brenner switch, treat this property as a boolean.

  property center

    Center parameter - should be negative

    This controls the addition of the -center parameter and its associated value. Set this property to the argument value required.

  property cluster

    Perform fast clustering of input sequences, use -tree1 to save tree

    This property controls the addition of the -cluster switch, treat this property as a boolean.

  property cluster1

    Clustering method used in iteration 1

    This controls the addition of the -cluster1 parameter and its associated value. Set this property to the argument value required.

  property cluster2

    Clustering method used in iteration 2

    This controls the addition of the -cluster2 parameter and its associated value. Set this property to the argument value required.

  property clw

    Write output in CLUSTALW format (with a MUSCLE header)

    This property controls the addition of the -clw switch, treat this property as a boolean.

  property clwout

    Write CLUSTALW output (with MUSCLE header) to specified filename

    This controls the addition of the -clwout parameter and its associated value. Set this property to the argument value required.

  property clwstrict

    Write output in CLUSTALW format with version 1.81 header

    This property controls the addition of the -clwstrict switch, treat this property as a boolean.

  property clwstrictout

    Write CLUSTALW output (with version 1.81 header) to specified filename

    This controls the addition of the -clwstrictout parameter and its associated value. Set this property to the argument value required.

  property core

    Do not catch exceptions

    This property controls the addition of the -core switch, treat this property as a boolean.

  property diagbreak

    Maximum distance between two diagonals that allows them to merge into one diagonal

    This controls the addition of the -diagbreak parameter and its associated value. Set this property to the argument value required.

  property diaglength

    Minimum length of diagonal

    This controls the addition of the -diaglength parameter and its associated value. Set this property to the argument value required.

  property diagmargin

    Discard this many positions at ends of diagonal

    This controls the addition of the -diagmargin parameter and its associated value. Set this property to the argument value required.

  property diags

    Find diagonals (faster for similar sequences)

    This property controls the addition of the -diags switch, treat this property as a boolean.

  property dimer

    Use faster (slightly less accurate) dimer approximationfor the SP score

    This property controls the addition of the -dimer switch, treat this property as a boolean.

  property distance1

    Distance measure for iteration 1

    This controls the addition of the -distance1 parameter and its associated value. Set this property to the argument value required.

  property distance2

    Distance measure for iteration 2

    This controls the addition of the -distance2 parameter and its associated value. Set this property to the argument value required.

  property fasta

    Write output in FASTA format

    This property controls the addition of the -fasta switch, treat this property as a boolean.

  property fastaout

    Write FASTA format output to specified filename

    This controls the addition of the -fastaout parameter and its associated value. Set this property to the argument value required.

  property gapextend

    Gap extension penalty

    This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

  property gapopen

    Gap open score - negative number

    This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

  property group

    Group similar sequences in output

    This property controls the addition of the -group switch, treat this property as a boolean.

  property html

    Write output in HTML format

    This property controls the addition of the -html switch, treat this property as a boolean.

  property htmlout

    Write HTML output to specified filename

    This controls the addition of the -htmlout parameter and its associated value. Set this property to the argument value required.

  property hydro

    Window size for hydrophobic region

    This controls the addition of the -hydro parameter and its associated value. Set this property to the argument value required.

  property hydrofactor

    Multiplier for gap penalties in hydrophobic regions

    This controls the addition of the -hydrofactor parameter and its associated value. Set this property to the argument value required.

  property in1

    First input filename for profile alignment

    This controls the addition of the -in1 parameter and its associated value. Set this property to the argument value required.

  property in2

    Second input filename for a profile alignment

    This controls the addition of the -in2 parameter and its associated value. Set this property to the argument value required.

  property input

    Input filename

    This controls the addition of the -in parameter and its associated value. Set this property to the argument value required.

  property le

    Use log-expectation profile score (VTML240)

    This property controls the addition of the -le switch, treat this property as a boolean.

  property log

    Log file name

    This controls the addition of the -log parameter and its associated value. Set this property to the argument value required.

  property loga

    Log file name (append to existing file)

    This controls the addition of the -loga parameter and its associated value. Set this property to the argument value required.

  property matrix

    path to NCBI or WU-BLAST format protein substitution matrix - also set -gapopen, -gapextend and -center

    This controls the addition of the -matrix parameter and its associated value. Set this property to the argument value required.

  property maxdiagbreak

    Deprecated in v3.8, use -diagbreak instead.

    This controls the addition of the -maxdiagbreak parameter and its associated value. Set this property to the argument value required.

  property maxhours

    Maximum time to run in hours

    This controls the addition of the -maxhours parameter and its associated value. Set this property to the argument value required.

  property maxiters

    Maximum number of iterations

    This controls the addition of the -maxiters parameter and its associated value. Set this property to the argument value required.

  property maxtrees

    Maximum number of trees to build in iteration 2

    This controls the addition of the -maxtrees parameter and its associated value. Set this property to the argument value required.

  property minbestcolscore

    Minimum score a column must have to be an anchor

    This controls the addition of the -minbestcolscore parameter and its associated value. Set this property to the argument value required.

  property minsmoothscore

    Minimum smoothed score a column must have to be an anchor

    This controls the addition of the -minsmoothscore parameter and its associated value. Set this property to the argument value required.

  property msf

    Write output in MSF format

    This property controls the addition of the -msf switch, treat this property as a boolean.

  property msfout

    Write MSF format output to specified filename

    This controls the addition of the -msfout parameter and its associated value. Set this property to the argument value required.

  property noanchors

    Do not use anchor optimisation in tree dependent refinement iterations

    This property controls the addition of the -noanchors switch, treat this property as a boolean.

  property nocore

    Catch exceptions

    This property controls the addition of the -nocore switch, treat this property as a boolean.

  property objscore

    Objective score used by tree dependent refinement

    This controls the addition of the -objscore parameter and its associated value. Set this property to the argument value required.

  property out

    Output filename

    This controls the addition of the -out parameter and its associated value. Set this property to the argument value required.

  property phyi

    Write output in PHYLIP interleaved format

    This property controls the addition of the -phyi switch, treat this property as a boolean.

  property phyiout

    Write PHYLIP interleaved output to specified filename

    This controls the addition of the -phyiout parameter and its associated value. Set this property to the argument value required.

  property phys

    Write output in PHYLIP sequential format

    This property controls the addition of the -phys switch, treat this property as a boolean.

  property physout

    Write PHYLIP sequential format to specified filename

    This controls the addition of the -physout parameter and its associated value. Set this property to the argument value required.

  property profile

    Perform a profile alignment

    This property controls the addition of the -profile switch, treat this property as a boolean.

  property quiet

    Do not display progress messages

    This property controls the addition of the -quiet switch, treat this property as a boolean.

  property refine

    Only do tree dependent refinement

    This property controls the addition of the -refine switch, treat this property as a boolean.

  property refinew

    Only do tree dependent refinement using sliding window approach

    This property controls the addition of the -refinew switch, treat this property as a boolean.

  property refinewindow

    Length of window for -refinew

    This controls the addition of the -refinewindow parameter and its associated value. Set this property to the argument value required.

  property root1

    Method used to root tree in iteration 1

    This controls the addition of the -root1 parameter and its associated value. Set this property to the argument value required.

  property root2

    Method used to root tree in iteration 2

    This controls the addition of the -root2 parameter and its associated value. Set this property to the argument value required.

  property scorefile

    Score file name, contains one line for each column in the alignment with average BLOSUM62 score

    This controls the addition of the -scorefile parameter and its associated value. Set this property to the argument value required.

  property seqtype

    Sequence type

    This controls the addition of the -seqtype parameter and its associated value. Set this property to the argument value required.

  property smoothscoreceil

    Maximum value of column score for smoothing

    This controls the addition of the -smoothscoreceil parameter and its associated value. Set this property to the argument value required.

  property smoothwindow

    Window used for anchor column smoothing

    This controls the addition of the -smoothwindow parameter and its associated value. Set this property to the argument value required.

  property sp

    Use sum-of-pairs protein profile score (PAM200)

    This property controls the addition of the -sp switch, treat this property as a boolean.

  property spn

    Use sum-of-pairs protein nucleotide profile score

    This property controls the addition of the -spn switch, treat this property as a boolean.

  property spscore

    Compute SP objective score of multiple alignment

    This controls the addition of the -spscore parameter and its associated value. Set this property to the argument value required.

  property stable

    Do not group similar sequences in output (not supported in v3.8)

    This property controls the addition of the -stable switch, treat this property as a boolean.

  property sueff

    Constant used in UPGMB clustering

    This controls the addition of the -sueff parameter and its associated value. Set this property to the argument value required.

  property sv

    Use sum-of-pairs profile score (VTML240)

    This property controls the addition of the -sv switch, treat this property as a boolean.

  property tree1

    Save Newick tree from iteration 1

    This controls the addition of the -tree1 parameter and its associated value. Set this property to the argument value required.

  property tree2

    Save Newick tree from iteration 2

    This controls the addition of the -tree2 parameter and its associated value. Set this property to the argument value required.

  property usetree

    Use given Newick tree as guide tree

    This controls the addition of the -usetree parameter and its associated value. Set this property to the argument value required.

  property verbose

    Write parameter settings and progress

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property version

    Write version string to stdout and exit

    This property controls the addition of the -version switch, treat this property as a boolean.

  property weight1

    Weighting scheme used in iteration 1

    This controls the addition of the -weight1 parameter and its associated value. Set this property to the argument value required.

  property weight2

    Weighting scheme used in iteration 2

    This controls the addition of the -weight2 parameter and its associated value. Set this property to the argument value required.

class Bio.Align.Applications.ClustalwCommandline(cmd='clustalw', **kwargs)

  Bases: `AbstractCommandline`

  Command line wrapper for clustalw (version one or two).

  http://www.clustal.org/

  Notes

  Last checked against versions: 1.83 and 2.1

  References

  Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.

  Examples

      >>> from Bio.Align.Applications import ClustalwCommandline
      >>> in_file = "unaligned.fasta"
      >>> clustalw_cline = ClustalwCommandline("clustalw2", infile=in_file)
      >>> print(clustalw_cline)
      clustalw2 -infile=unaligned.fasta

  You would typically run the command line with clustalw_cline() or via the Python subprocess module, as described in the Biopython tutorial.

  __init__(cmd='clustalw', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 16
  __static_attributes__ = ('parameters',)
  property align

    Do full multiple alignment.

    This property controls the addition of the -align switch, treat this property as a boolean.

  property bootlabels

    Node OR branch position of bootstrap values in tree display

    This controls the addition of the -bootlabels parameter and its associated value. Set this property to the argument value required.

  property bootstrap

    Bootstrap a NJ tree (n= number of bootstraps; def. = 1000).

    This controls the addition of the -bootstrap parameter and its associated value. Set this property to the argument value required.

  property case

    LOWER or UPPER (for GDE output only)

    This controls the addition of the -case parameter and its associated value. Set this property to the argument value required.

  property check

    Outline the command line params.

    This property controls the addition of the -check switch, treat this property as a boolean.

  property clustering

    NJ or UPGMA

    This controls the addition of the -clustering parameter and its associated value. Set this property to the argument value required.

  property convert

    Output the input sequences in a different file format.

    This property controls the addition of the -convert switch, treat this property as a boolean.

  property dnamatrix

    DNA weight matrix=IUB, CLUSTALW or filename

    This controls the addition of the -dnamatrix parameter and its associated value. Set this property to the argument value required.

  property endgaps

    No end gap separation pen.

    This property controls the addition of the -endgaps switch, treat this property as a boolean.

  property fullhelp

    Output full help content.

    This property controls the addition of the -fullhelp switch, treat this property as a boolean.

  property gapdist

    Gap separation pen. range

    This controls the addition of the -gapdist parameter and its associated value. Set this property to the argument value required.

  property gapext

    Gap extension penalty

    This controls the addition of the -gapext parameter and its associated value. Set this property to the argument value required.

  property gapopen

    Gap opening penalty

    This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

  property helixendin

    Number of residues inside helix to be treated as terminal

    This controls the addition of the -helixendin parameter and its associated value. Set this property to the argument value required.

  property helixendout

    Number of residues outside helix to be treated as terminal

    This controls the addition of the -helixendout parameter and its associated value. Set this property to the argument value required.

  property helixgap

    Gap penalty for helix core residues

    This controls the addition of the -helixgap parameter and its associated value. Set this property to the argument value required.

  property help

    Outline the command line params.

    This property controls the addition of the -help switch, treat this property as a boolean.

  property hgapresidues

    List hydrophilic res.

    This property controls the addition of the -hgapresidues switch, treat this property as a boolean.

  property infile

    Input sequences.

    This controls the addition of the -infile parameter and its associated value. Set this property to the argument value required.

  property iteration

    NONE or TREE or ALIGNMENT

    This controls the addition of the -iteration parameter and its associated value. Set this property to the argument value required.

  property kimura

    Use Kimura’s correction.

    This property controls the addition of the -kimura switch, treat this property as a boolean.

  property ktuple

    Word size

    This controls the addition of the -ktuple parameter and its associated value. Set this property to the argument value required.

  property loopgap

    Gap penalty for loop regions

    This controls the addition of the -loopgap parameter and its associated value. Set this property to the argument value required.

  property matrix

    Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename

    This controls the addition of the -matrix parameter and its associated value. Set this property to the argument value required.

  property maxdiv

    % ident. for delay

    This controls the addition of the -maxdiv parameter and its associated value. Set this property to the argument value required.

  property maxseqlen

    Maximum allowed input sequence length

    This controls the addition of the -maxseqlen parameter and its associated value. Set this property to the argument value required.

  property negative

    Protein alignment with negative values in matrix

    This property controls the addition of the -negative switch, treat this property as a boolean.

  property newtree

    Output file name for newly created guide tree

    This controls the addition of the -newtree parameter and its associated value. Set this property to the argument value required.

  property newtree1

    Output file name for new guide tree of profile1

    This controls the addition of the -newtree1 parameter and its associated value. Set this property to the argument value required.

  property newtree2

    Output file for new guide tree of profile2

    This controls the addition of the -newtree2 parameter and its associated value. Set this property to the argument value required.

  property nohgap

    Hydrophilic gaps off

    This property controls the addition of the -nohgap switch, treat this property as a boolean.

  property nopgap

    Residue-specific gaps off

    This property controls the addition of the -nopgap switch, treat this property as a boolean.

  property nosecstr1

    Do not use secondary structure-gap penalty mask for profile 1

    This property controls the addition of the -nosecstr1 switch, treat this property as a boolean.

  property nosecstr2

    Do not use secondary structure-gap penalty mask for profile 2

    This property controls the addition of the -nosecstr2 switch, treat this property as a boolean.

  property noweights

    Disable sequence weighting

    This property controls the addition of the -noweights switch, treat this property as a boolean.

  property numiter

    maximum number of iterations to perform

    This controls the addition of the -numiter parameter and its associated value. Set this property to the argument value required.

  property options

    List the command line parameters

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output sequence alignment file name

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property outorder

    Output taxon order: INPUT or ALIGNED

    This controls the addition of the -outorder parameter and its associated value. Set this property to the argument value required.

  property output

    Output format: CLUSTAL(default), GCG, GDE, PHYLIP, PIR, NEXUS and FASTA

    This controls the addition of the -output parameter and its associated value. Set this property to the argument value required.

  property outputtree

    nj OR phylip OR dist OR nexus

    This controls the addition of the -outputtree parameter and its associated value. Set this property to the argument value required.

  property pairgap

    Gap penalty

    This controls the addition of the -pairgap parameter and its associated value. Set this property to the argument value required.

  property pim

    Output percent identity matrix (while calculating the tree).

    This property controls the addition of the -pim switch, treat this property as a boolean.

  property profile

    Merge two alignments by profile alignment

    This property controls the addition of the -profile switch, treat this property as a boolean.

  property profile1

    Profiles (old alignment).

    This controls the addition of the -profile1 parameter and its associated value. Set this property to the argument value required.

  property profile2

    Profiles (old alignment).

    This controls the addition of the -profile2 parameter and its associated value. Set this property to the argument value required.

  property pwdnamatrix

    DNA weight matrix=IUB, CLUSTALW or filename

    This controls the addition of the -pwdnamatrix parameter and its associated value. Set this property to the argument value required.

  property pwgapext

    Gap extension penalty

    This controls the addition of the -pwgapext parameter and its associated value. Set this property to the argument value required.

  property pwgapopen

    Gap opening penalty

    This controls the addition of the -pwgapopen parameter and its associated value. Set this property to the argument value required.

  property pwmatrix

    Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename

    This controls the addition of the -pwmatrix parameter and its associated value. Set this property to the argument value required.

  property quicktree

    Use FAST algorithm for the alignment guide tree

    This property controls the addition of the -quicktree switch, treat this property as a boolean.

  property quiet

    Reduce console output to minimum

    This property controls the addition of the -quiet switch, treat this property as a boolean.

  property range

    Sequence range to write starting m to m+n. Input as string eg. ‘24,200’

    This controls the addition of the -range parameter and its associated value. Set this property to the argument value required.

  property score

    Either: PERCENT or ABSOLUTE

    This controls the addition of the -score parameter and its associated value. Set this property to the argument value required.

  property secstrout

    STRUCTURE or MASK or BOTH or NONE output in alignment file

    This controls the addition of the -secstrout parameter and its associated value. Set this property to the argument value required.

  property seed

    Seed number for bootstraps.

    This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.

  property seqno_range

    OFF or ON (NEW- for all output formats)

    This controls the addition of the -seqno_range parameter and its associated value. Set this property to the argument value required.

  property seqnos

    OFF or ON (for Clustal output only)

    This controls the addition of the -seqnos parameter and its associated value. Set this property to the argument value required.

  property sequences

    Sequentially add profile2 sequences to profile1 alignment

    This property controls the addition of the -sequences switch, treat this property as a boolean.

  property stats

    Log some alignment statistics to file

    This controls the addition of the -stats parameter and its associated value. Set this property to the argument value required.

  property strandendin

    Number of residues inside strand to be treated as terminal

    This controls the addition of the -strandendin parameter and its associated value. Set this property to the argument value required.

  property strandendout

    Number of residues outside strand to be treated as terminal

    This controls the addition of the -strandendout parameter and its associated value. Set this property to the argument value required.

  property strandgap

    gap penalty for strand core residues

    This controls the addition of the -strandgap parameter and its associated value. Set this property to the argument value required.

  property terminalgap

    Gap penalty for structure termini

    This controls the addition of the -terminalgap parameter and its associated value. Set this property to the argument value required.

  property topdiags

    Number of best diags.

    This controls the addition of the -topdiags parameter and its associated value. Set this property to the argument value required.

  property tossgaps

    Ignore positions with gaps.

    This property controls the addition of the -tossgaps switch, treat this property as a boolean.

  property transweight

    Transitions weighting

    This controls the addition of the -transweight parameter and its associated value. Set this property to the argument value required.

  property tree

    Calculate NJ tree.

    This property controls the addition of the -tree switch, treat this property as a boolean.

  property type

    PROTEIN or DNA sequences

    This controls the addition of the -type parameter and its associated value. Set this property to the argument value required.

  property usetree

    File name of guide tree

    This controls the addition of the -usetree parameter and its associated value. Set this property to the argument value required.

  property usetree1

    File name of guide tree for profile1

    This controls the addition of the -usetree1 parameter and its associated value. Set this property to the argument value required.

  property usetree2

    File name of guide tree for profile2

    This controls the addition of the -usetree2 parameter and its associated value. Set this property to the argument value required.

  property window

    Window around best diags.

    This controls the addition of the -window parameter and its associated value. Set this property to the argument value required.

class Bio.Align.Applications.ClustalOmegaCommandline(cmd='clustalo', **kwargs)

  Bases: `AbstractCommandline`

  Command line wrapper for clustal omega.

  http://www.clustal.org/omega

  Notes

  Last checked against version: 1.2.0

  References

  Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7:539 https://doi.org/10.1038/msb.2011.75

  Examples

      >>> from Bio.Align.Applications import ClustalOmegaCommandline
      >>> in_file = "unaligned.fasta"
      >>> out_file = "aligned.fasta"
      >>> clustalomega_cline = ClustalOmegaCommandline(infile=in_file, outfile=out_file, verbose=True, auto=True)
      >>> print(clustalomega_cline)
      clustalo -i unaligned.fasta -o aligned.fasta --auto -v

  You would typically run the command line with clustalomega_cline() or via the Python subprocess module, as described in the Biopython tutorial.

  __init__(cmd='clustalo', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 15
  __static_attributes__ = ('parameters',)
  property auto

    Set options automatically (might overwrite some of your options)

    This property controls the addition of the –auto switch, treat this property as a boolean.

  property clusteringout

    Clustering output file

    This controls the addition of the –clustering-out parameter and its associated value. Set this property to the argument value required.

  property clustersize

    soft maximum of sequences in sub-clusters

    This controls the addition of the –cluster-size parameter and its associated value. Set this property to the argument value required.

  property dealign

    Dealign input sequences

    This property controls the addition of the –dealign switch, treat this property as a boolean.

  property distmat_full

    Use full distance matrix for guide-tree calculation (slow; mBed is default)

    This property controls the addition of the –full switch, treat this property as a boolean.

  property distmat_full_iter

    Use full distance matrix for guide-tree calculation during iteration (mBed is default)

    This property controls the addition of the –full-iter switch, treat this property as a boolean.

  property distmat_in

    Pairwise distance matrix input file (skips distance computation).

    This controls the addition of the –distmat-in parameter and its associated value. Set this property to the argument value required.

  property distmat_out

    Pairwise distance matrix output file.

    This controls the addition of the –distmat-out parameter and its associated value. Set this property to the argument value required.

  property force

    Force file overwriting.

    This property controls the addition of the –force switch, treat this property as a boolean.

  property guidetree_in

    Guide tree input file (skips distance computation and guide-tree clustering step).

    This controls the addition of the –guidetree-in parameter and its associated value. Set this property to the argument value required.

  property guidetree_out

    Guide tree output file.

    This controls the addition of the –guidetree-out parameter and its associated value. Set this property to the argument value required.

  property help

    Print help and exit.

    This property controls the addition of the -h switch, treat this property as a boolean.

  property hmm_input

    HMM input files

    This controls the addition of the –hmm-in parameter and its associated value. Set this property to the argument value required.

  property infile

    Multiple sequence input file

    This controls the addition of the -i parameter and its associated value. Set this property to the argument value required.

  property infmt

    Forced sequence input file format (default: auto)

    > Allowed values: a2m, fa[sta], clu[stal], msf, phy[lip], selex, st[ockholm], vie[nna]

    This controls the addition of the –infmt parameter and its associated value. Set this property to the argument value required.

  property isprofile

    disable check if profile, force profile (default no)

    This property controls the addition of the –is-profile switch, treat this property as a boolean.

  property iterations

    Number of (combined guide-tree/HMM) iterations

    This controls the addition of the –iterations parameter and its associated value. Set this property to the argument value required.

  property log

    Log all non-essential output to this file.

    This controls the addition of the -l parameter and its associated value. Set this property to the argument value required.

  property long_version

    Print long version information and exit

    This property controls the addition of the –long-version switch, treat this property as a boolean.

  property max_guidetree_iterations

    Maximum number of guidetree iterations

    This controls the addition of the –max-guidetree-iterations parameter and its associated value. Set this property to the argument value required.

  property max_hmm_iterations

    Maximum number of HMM iterations

    This controls the addition of the –max-hmm-iterations parameter and its associated value. Set this property to the argument value required.

  property maxnumseq

    Maximum allowed number of sequences

    This controls the addition of the –maxnumseq parameter and its associated value. Set this property to the argument value required.

  property maxseqlen

    Maximum allowed sequence length

    This controls the addition of the –maxseqlen parameter and its associated value. Set this property to the argument value required.

  property outfile

    Multiple sequence alignment output file (default: stdout).

    This controls the addition of the -o parameter and its associated value. Set this property to the argument value required.

  property outfmt

    MSA output file format: a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna] (default: fasta).

    This controls the addition of the –outfmt parameter and its associated value. Set this property to the argument value required.

  property outputorder

    MSA output order like in input/guide-tree

    This controls the addition of the –output-order parameter and its associated value. Set this property to the argument value required.

  property percentid

    convert distances into percent identities (default no)

    This property controls the addition of the –percent-id switch, treat this property as a boolean.

  property profile1

    Pre-aligned multiple sequence file (aligned columns will be kept fix).

    This controls the addition of the –profile1 parameter and its associated value. Set this property to the argument value required.

  property profile2

    Pre-aligned multiple sequence file (aligned columns will be kept fix).

    This controls the addition of the –profile2 parameter and its associated value. Set this property to the argument value required.

  property residuenumber

    in Clustal format print residue numbers (default no)

    This property controls the addition of the –residuenumber switch, treat this property as a boolean.

  property seqtype

    {Protein, RNA, DNA} Force a sequence type (default: auto).

    This controls the addition of the -t parameter and its associated value. Set this property to the argument value required.

  property threads

    Number of processors to use

    This controls the addition of the –threads parameter and its associated value. Set this property to the argument value required.

  property usekimura

    use Kimura distance correction for aligned sequences (default no)

    This property controls the addition of the –use-kimura switch, treat this property as a boolean.

  property verbose

    Verbose output

    This property controls the addition of the -v switch, treat this property as a boolean.

  property version

    Print version information and exit

    This property controls the addition of the –version switch, treat this property as a boolean.

  property wrap

    number of residues before line-wrap in output

    This controls the addition of the –wrap parameter and its associated value. Set this property to the argument value required.

class Bio.Align.Applications.PrankCommandline(cmd='prank', **kwargs)

  Bases: `AbstractCommandline`

  Command line wrapper for the multiple alignment program PRANK.

  http://www.ebi.ac.uk/goldman-srv/prank/prank/

  Notes

  Last checked against version: 081202

  References

  Loytynoja, A. and Goldman, N. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences, 102: 10557–10562.

  Loytynoja, A. and Goldman, N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320: 1632.

  Examples

  To align a FASTA file (unaligned.fasta) with the output in aligned FASTA format with the output filename starting with “aligned” (you can’t pick the filename explicitly), no tree output and no XML output, use:

      >>> from Bio.Align.Applications import PrankCommandline
      >>> prank_cline = PrankCommandline(d="unaligned.fasta",
      ...                                o="aligned", # prefix only!
      ...                                f=8, # FASTA output
      ...                                notree=True, noxml=True)
      >>> print(prank_cline)
      prank -d=unaligned.fasta -o=aligned -f=8 -noxml -notree

  You would typically run the command line with prank_cline() or via the Python subprocess module, as described in the Biopython tutorial.

  __init__(cmd='prank', **kwargs)

    Initialize the class.

  property F

    Force insertions to be always skipped: same as +F

    This property controls the addition of the -F switch, treat this property as a boolean.

  __annotations__ = {}
  __firstlineno__ = 14
  __static_attributes__ = ('parameters',)
  property codon

    Codon aware alignment or not

    This property controls the addition of the -codon switch, treat this property as a boolean.

  property convert

    Convert input alignment to new format. Do not perform alignment

    This property controls the addition of the -convert switch, treat this property as a boolean.

  property d

    Input filename

    This controls the addition of the -d parameter and its associated value. Set this property to the argument value required.

  property dnafreqs

    DNA frequencies - ‘A,C,G,T’. eg ‘25,25,25,25’ as a quote surrounded string value. Default: empirical

    This controls the addition of the -dnafreqs parameter and its associated value. Set this property to the argument value required.

  property dots

    Show insertion gaps as dots

    This property controls the addition of the -dots switch, treat this property as a boolean.

  property f

    Output alignment format. Default: 8 FASTA Option are: 1. IG/Stanford 8. Pearson/Fasta 2. GenBank/GB 11. Phylip3.2 3. NBRF 12. Phylip 4. EMBL 14. PIR/CODATA 6. DNAStrider 15. MSF 7. Fitch 17. PAUP/NEXUS

    This controls the addition of the -f parameter and its associated value. Set this property to the argument value required.

  property fixedbranches

    Use fixed branch lengths of input value

    This controls the addition of the -fixedbranches parameter and its associated value. Set this property to the argument value required.

  property gapext

    Gap extension probability. Default: dna 0.5 / prot 0.5

    This controls the addition of the -gapext parameter and its associated value. Set this property to the argument value required.

  property gaprate

    Gap opening rate. Default: dna 0.025 prot 0.0025

    This controls the addition of the -gaprate parameter and its associated value. Set this property to the argument value required.

  property kappa

    Transition/transversion ratio. Default: 2

    This controls the addition of the -kappa parameter and its associated value. Set this property to the argument value required.

  property longseq

    Save space in pairwise alignments

    This property controls the addition of the -longseq switch, treat this property as a boolean.

  property m

    User-defined alignment model filename. Default: HKY2/WAG

    This controls the addition of the -m parameter and its associated value. Set this property to the argument value required.

  property matinitsize

    Matrix initial size multiplier

    This controls the addition of the -matinitsize parameter and its associated value. Set this property to the argument value required.

  property matresize

    Matrix resizing multiplier

    This controls the addition of the -matresize parameter and its associated value. Set this property to the argument value required.

  property maxbranches

    Use maximum branch lengths of input value

    This controls the addition of the -maxbranches parameter and its associated value. Set this property to the argument value required.

  property mttranslate

    Translate to protein using mt table

    This property controls the addition of the -mttranslate switch, treat this property as a boolean.

  property nopost

    Do not compute posterior support. Default: compute

    This property controls the addition of the -nopost switch, treat this property as a boolean.

  property notree

    Do not output dnd tree files (PRANK versions earlier than v.120626)

    This property controls the addition of the -notree switch, treat this property as a boolean.

  property noxml

    Do not output XML files (PRANK versions earlier than v.120626)

    This property controls the addition of the -noxml switch, treat this property as a boolean.

  property o
    Output filenames prefix. Default: ‘output’

      Will write: output.?.fas (depending on requested format), output.?.xml and output.?.dnd

    This controls the addition of the -o parameter and its associated value. Set this property to the argument value required.

  property once

    Run only once. Default: twice if no guidetree given

    This property controls the addition of the -once switch, treat this property as a boolean.

  property printnodes

    Output each node; mostly for debugging

    This property controls the addition of the -printnodes switch, treat this property as a boolean.

  property pwdist

    Expected pairwise distance for computing guidetree. Default: dna 0.25 / prot 0.5

    This controls the addition of the -pwdist parameter and its associated value. Set this property to the argument value required.

  property pwgenomic

    Do pairwise alignment, no guidetree

    This property controls the addition of the -pwgenomic switch, treat this property as a boolean.

  property pwgenomicdist

    Distance for pairwise alignment. Default: 0.3

    This controls the addition of the -pwgenomicdist parameter and its associated value. Set this property to the argument value required.

  property quiet

    Reduce verbosity

    This property controls the addition of the -quiet switch, treat this property as a boolean.

  property realbranches

    Disable branch length truncation

    This property controls the addition of the -realbranches switch, treat this property as a boolean.

  property rho

    Purine/pyrimidine ratio. Default: 1

    This controls the addition of the -rho parameter and its associated value. Set this property to the argument value required.

  property scalebranches

    Scale branch lengths. Default: dna 1 / prot 2

    This controls the addition of the -scalebranches parameter and its associated value. Set this property to the argument value required.

  property shortnames

    Truncate names at first space

    This property controls the addition of the -shortnames switch, treat this property as a boolean.

  property showtree

    Output dnd tree files (PRANK v.120626 and later)

    This property controls the addition of the -showtree switch, treat this property as a boolean.

  property showxml

    Output XML files (PRANK v.120626 and later)

    This property controls the addition of the -showxml switch, treat this property as a boolean.

  property skipins

    Skip insertions in posterior support

    This property controls the addition of the -skipins switch, treat this property as a boolean.

  property t

    Input guide tree filename

    This controls the addition of the -t parameter and its associated value. Set this property to the argument value required.

  property termgap

    Penalise terminal gaps normally

    This property controls the addition of the -termgap switch, treat this property as a boolean.

  property translate

    Translate to protein

    This property controls the addition of the -translate switch, treat this property as a boolean.

  property tree

    Input guide tree as Newick string

    This controls the addition of the -tree parameter and its associated value. Set this property to the argument value required.

  property twice

    Always run twice

    This property controls the addition of the -twice switch, treat this property as a boolean.

  property uselogs

    Slower but should work for a greater number of sequences

    This property controls the addition of the -uselogs switch, treat this property as a boolean.

  property writeanc

    Output ancestral sequences

    This property controls the addition of the -writeanc switch, treat this property as a boolean.

class Bio.Align.Applications.MafftCommandline(cmd='mafft', **kwargs)

  Bases: `AbstractCommandline`

  Command line wrapper for the multiple alignment program MAFFT.

  http://align.bmr.kyushu-u.ac.jp/mafft/software/

  Notes

  Last checked against version: MAFFT v6.717b (2009/12/03)

  References

  Katoh, Toh (BMC Bioinformatics 9:212, 2008) Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (describes RNA structural alignment methods)

  Katoh, Toh (Briefings in Bioinformatics 9:286-298, 2008) Recent developments in the MAFFT multiple sequence alignment program (outlines version 6)

  Katoh, Toh (Bioinformatics 23:372-374, 2007) Errata PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm)

  Katoh, Kuma, Toh, Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies)

  Katoh, Misawa, Kuma, Miyata (Nucleic Acids Res. 30:3059-3066, 2002)

  Examples

      >>> from Bio.Align.Applications import MafftCommandline
      >>> mafft_exe = "/opt/local/mafft"
      >>> in_file = "../Doc/examples/opuntia.fasta"
      >>> mafft_cline = MafftCommandline(mafft_exe, input=in_file)
      >>> print(mafft_cline)
      /opt/local/mafft ../Doc/examples/opuntia.fasta

  If the mafft binary is on the path (typically the case on a Unix style operating system) then you don’t need to supply the executable location:

      >>> from Bio.Align.Applications import MafftCommandline
      >>> in_file = "../Doc/examples/opuntia.fasta"
      >>> mafft_cline = MafftCommandline(input=in_file)
      >>> print(mafft_cline)
      mafft ../Doc/examples/opuntia.fasta

  You would typically run the command line with mafft_cline() or via the Python subprocess module, as described in the Biopython tutorial.

  Note that MAFFT will write the alignment to stdout, which you may want to save to a file and then parse, e.g.:

      stdout, stderr = mafft_cline()
      with open("aligned.fasta", "w") as handle:
          handle.write(stdout)
      from Bio import AlignIO
      align = AlignIO.read("aligned.fasta", "fasta")

  Alternatively, to parse the output with AlignIO directly you can use StringIO to turn the string into a handle:

      stdout, stderr = mafft_cline()
      from io import StringIO
      from Bio import AlignIO
      align = AlignIO.read(StringIO(stdout), "fasta")

  __init__(cmd='mafft', **kwargs)

    Initialize the class.

  property LEXP

    Gap extension penalty to skip the alignment. Default: 0.00

    This controls the addition of the –LEXP parameter and its associated value. Set this property to the argument value required.

  property LOP

    Gap opening penalty to skip the alignment. Default: -6.00

    This controls the addition of the –LOP parameter and its associated value. Set this property to the argument value required.

  __annotations__ = {}
  __firstlineno__ = 15
  __static_attributes__ = ('parameters',)
  property aamatrix

    Use a user-defined AA scoring matrix. Default: BLOSUM62

    This controls the addition of the –aamatrix parameter and its associated value. Set this property to the argument value required.

  property adjustdirection

    Adjust direction according to the first sequence. Default off.

    This property controls the addition of the –adjustdirection switch, treat this property as a boolean.

  property adjustdirectionaccurately

    Adjust direction according to the first sequence,for highly diverged data; very slowDefault off.

    This property controls the addition of the –adjustdirectionaccurately switch, treat this property as a boolean.

  property amino

    Assume the sequences are amino acid (True/False). Default: auto

    This property controls the addition of the –amino switch, treat this property as a boolean.

  property auto

    Automatically select strategy. Default off.

    This property controls the addition of the –auto switch, treat this property as a boolean.

  property bl

    BLOSUM number matrix is used. Default: 62

    This controls the addition of the –bl parameter and its associated value. Set this property to the argument value required.

  property clustalout

    Output format: clustal (True) or fasta (False, default)

    This property controls the addition of the –clustalout switch, treat this property as a boolean.

  property dpparttree

    The PartTree algorithm is used with distances based on DP. Default: off

    This property controls the addition of the –dpparttree switch, treat this property as a boolean.

  property ep

    Offset value, which works like gap extension penalty, for group-to- group alignment. Default: 0.123

    This controls the addition of the –ep parameter and its associated value. Set this property to the argument value required.

  property fastapair

    All pairwise alignments are computed with FASTA (Pearson and Lipman 1988). Default: off

    This property controls the addition of the –fastapair switch, treat this property as a boolean.

  property fastaparttree

    The PartTree algorithm is used with distances based on FASTA. Default: off

    This property controls the addition of the –fastaparttree switch, treat this property as a boolean.

  property fft

    Use FFT approximation in group-to-group alignment. Default: on

    This property controls the addition of the –fft switch, treat this property as a boolean.

  property fmodel

    Incorporate the AA/nuc composition information into the scoring matrix (True) or not (False, default)

    This property controls the addition of the –fmodel switch, treat this property as a boolean.

  property genafpair

    All pairwise alignments are computed with a local algorithm with the generalized affine gap cost (Altschul 1998). Default: off

    This property controls the addition of the –genafpair switch, treat this property as a boolean.

  property globalpair

    All pairwise alignments are computed with the Needleman-Wunsch algorithm. Default: off

    This property controls the addition of the –globalpair switch, treat this property as a boolean.

  property groupsize

    Do not make alignment larger than number sequences. Default: the number of input sequences

    This property controls the addition of the –groupsize switch, treat this property as a boolean.

  property input

    Input file name

    This controls the addition of the input parameter and its associated value. Set this property to the argument value required.

  property input1

    Second input file name for the mafft-profile command

    This controls the addition of the input1 parameter and its associated value. Set this property to the argument value required.

  property inputorder

    Output order: same as input (True, default) or alignment based (False)

    This property controls the addition of the –inputorder switch, treat this property as a boolean.

  property jtt

    JTT PAM number (Jones et al. 1992) matrix is used. number>0. Default: BLOSUM62

    This controls the addition of the –jtt parameter and its associated value. Set this property to the argument value required.

  property lep

    Offset value at local pairwise alignment. Default: 0.1

    This controls the addition of the –lep parameter and its associated value. Set this property to the argument value required.

  property lexp

    Gap extension penalty at local pairwise alignment. Default: -0.1

    This controls the addition of the –lexp parameter and its associated value. Set this property to the argument value required.

  property localpair

    All pairwise alignments are computed with the Smith-Waterman algorithm. Default: off

    This property controls the addition of the –localpair switch, treat this property as a boolean.

  property lop

    Gap opening penalty at local pairwise alignment. Default: 0.123

    This controls the addition of the –lop parameter and its associated value. Set this property to the argument value required.

  property maxiterate

    Number cycles of iterative refinement are performed. Default: 0

    This controls the addition of the –maxiterate parameter and its associated value. Set this property to the argument value required.

  property memsave

    Use the Myers-Miller (1988) algorithm. Default: automatically turned on when the alignment length exceeds 10,000 (aa/nt).

    This property controls the addition of the –memsave switch, treat this property as a boolean.

  property namelength

    Name length in CLUSTAL and PHYLIP output.

    > MAFFT v6.847 (2011) added –namelength for use with the –clustalout option for CLUSTAL output.

    > MAFFT v7.024 (2013) added support for this with the –phylipout option for PHYLIP output (default 10).

    This controls the addition of the –namelength parameter and its associated value. Set this property to the argument value required.

  property nofft

    Do not use FFT approximation in group-to-group alignment. Default: off

    This property controls the addition of the –nofft switch, treat this property as a boolean.

  property noscore

    Alignment score is not checked in the iterative refinement stage. Default: off (score is checked)

    This property controls the addition of the –noscore switch, treat this property as a boolean.

  property nuc

    Assume the sequences are nucleotide (True/False). Default: auto

    This property controls the addition of the –nuc switch, treat this property as a boolean.

  property op

    Gap opening penalty at group-to-group alignment. Default: 1.53

    This controls the addition of the –op parameter and its associated value. Set this property to the argument value required.

  property partsize

    The number of partitions in the PartTree algorithm. Default: 50

    This controls the addition of the –partsize parameter and its associated value. Set this property to the argument value required.

  property parttree

    Use a fast tree-building method with the 6mer distance. Default: off

    This property controls the addition of the –parttree switch, treat this property as a boolean.

  property phylipout

    Output format: phylip (True), or fasta (False, default)

    This property controls the addition of the –phylipout switch, treat this property as a boolean.

  property quiet

    Do not report progress (True) or not (False, default).

    This property controls the addition of the –quiet switch, treat this property as a boolean.

  property reorder

    Output order: aligned (True) or in input order (False, default)

    This property controls the addition of the –reorder switch, treat this property as a boolean.

  property retree

    Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2

    This controls the addition of the –retree parameter and its associated value. Set this property to the argument value required.

  property seed

    Seed alignments given in alignment_n (fasta format) are aligned with sequences in input.

    This controls the addition of the –seed parameter and its associated value. Set this property to the argument value required.

  property sixmerpair

    Distance is calculated based on the number of shared 6mers. Default: on

    This property controls the addition of the –6merpair switch, treat this property as a boolean.

  property thread

    Number of threads to use. Default: 1

    This controls the addition of the –thread parameter and its associated value. Set this property to the argument value required.

  property tm

    Transmembrane PAM number (Jones et al. 1994) matrix is used. number>0. Default: BLOSUM62

    This controls the addition of the –tm parameter and its associated value. Set this property to the argument value required.

  property treeout

    Guide tree is output to the input.tree file (True) or not (False, default)

    This property controls the addition of the –treeout switch, treat this property as a boolean.

  property weighti

    Weighting factor for the consistency term calculated from pairwise alignments. Default: 2.7

    This controls the addition of the –weighti parameter and its associated value. Set this property to the argument value required.

class Bio.Align.Applications.DialignCommandline(cmd='dialign2-2', **kwargs)

  Bases: `AbstractCommandline`

  Command line wrapper for the multiple alignment program DIALIGN2-2.

  http://bibiserv.techfak.uni-bielefeld.de/dialign/welcome.html

  Notes

  Last checked against version: 2.2

  References

  B. Morgenstern (2004). DIALIGN: Multiple DNA and Protein Sequence Alignment at BiBiServ. Nucleic Acids Research 32, W33-W36.

  Examples

  To align a FASTA file (unaligned.fasta) with the output files names aligned.* including a FASTA output file (aligned.fa), use:

      >>> from Bio.Align.Applications import DialignCommandline
      >>> dialign_cline = DialignCommandline(input="unaligned.fasta",
      ...                                    fn="aligned", fa=True)
      >>> print(dialign_cline)
      dialign2-2 -fa -fn aligned unaligned.fasta

  You would typically run the command line with dialign_cline() or via the Python subprocess module, as described in the Biopython tutorial.

  __init__(cmd='dialign2-2', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 15
  __static_attributes__ = ('parameters', 'program_name')
  property afc

    Creates additional output file ‘*.afc’ containing data of all fragments considered for alignment WARNING: this file can be HUGE !

    This property controls the addition of the -afc switch, treat this property as a boolean.

  property afc_v

    Like ‘-afc’ but verbose: fragments are explicitly printed. WARNING: this file can be EVEN BIGGER !

    This property controls the addition of the -afc_v switch, treat this property as a boolean.

  property anc

    Anchored alignment. Requires a file <seq_file>.anc containing anchor points.

    This property controls the addition of the -anc switch, treat this property as a boolean.

  property cs

    If segments are translated, not only the ‘Watson strand’ but also the ‘Crick strand’ is looked at.

    This property controls the addition of the -cs switch, treat this property as a boolean.

  property cw

    Additional output file in CLUSTAL W format.

    This property controls the addition of the -cw switch, treat this property as a boolean.

  property ds

    ‘dna alignment speed up’ - non-translated nucleic acid fragments are taken into account only if they start with at least two matches. Speeds up DNA alignment at the expense of sensitivity.

    This property controls the addition of the -ds switch, treat this property as a boolean.

  property fa

    Additional output file in FASTA format.

    This property controls the addition of the -fa switch, treat this property as a boolean.

  property ff

    Creates file *.frg containing information about all fragments that are part of the respective optimal pairwise alignmnets plus information about consistency in the multiple alignment

    This property controls the addition of the -ff switch, treat this property as a boolean.

  property fn

    Output files are named <out_file>.<extension>.

    This controls the addition of the -fn parameter and its associated value. Set this property to the argument value required.

  property fop

    Creates file *.fop containing coordinates of all fragments that are part of the respective pairwise alignments.

    This property controls the addition of the -fop switch, treat this property as a boolean.

  property fsm

    Creates file *.fsm containing coordinates of all fragments that are part of the final alignment

    This property controls the addition of the -fsm switch, treat this property as a boolean.

  property input

    Input file name. Must be FASTA format

    This controls the addition of the input parameter and its associated value. Set this property to the argument value required.

  property iw

    Overlap weights switched off (by default, overlap weights are used if up to 35 sequences are aligned). This option speeds up the alignment but may lead to reduced alignment quality.

    This property controls the addition of the -iw switch, treat this property as a boolean.

  property lgs

    ‘long genomic sequences’ - combines the following options: -ma, -thr 2, -lmax 30, -smin 8, -nta, -ff, -fop, -ff, -cs, -ds, -pst

    This property controls the addition of the -lgs switch, treat this property as a boolean.

  property lgs_t

    Like ‘-lgs’ but with all segment pairs assessed at the peptide level (rather than ‘mixed alignments’ as with the ‘-lgs’ option). Therefore faster than -lgs but not very sensitive for non-coding regions.

    This property controls the addition of the -lgs_t switch, treat this property as a boolean.

  property lmax

    Maximum fragment length = x (default: x = 40 or x = 120 for ‘translated’ fragments). Shorter x speeds up the program but may affect alignment quality.

    This controls the addition of the -lmax parameter and its associated value. Set this property to the argument value required.

  property lo

    (Long Output) Additional file *.log with information about fragments selected for pairwise alignment and about consistency in multi-alignment procedure.

    This property controls the addition of the -lo switch, treat this property as a boolean.

  property ma

    ‘mixed alignments’ consisting of P-fragments and N-fragments if nucleic acid sequences are aligned.

    This property controls the addition of the -ma switch, treat this property as a boolean.

  property mask

    Residues not belonging to selected fragments are replaced by ‘*’ characters in output alignment (rather than being printed in lower-case characters)

    This property controls the addition of the -mask switch, treat this property as a boolean.

  property mat

    Creates file *mat with substitution counts derived from the fragments that have been selected for alignment.

    This property controls the addition of the -mat switch, treat this property as a boolean.

  property mat_thr

    Like ‘-mat’ but only fragments with weight score > t are considered

    This property controls the addition of the -mat_thr switch, treat this property as a boolean.

  property max_link

    ‘maximum linkage’ clustering used to construct sequence tree (instead of UPGMA).

    This property controls the addition of the -max_link switch, treat this property as a boolean.

  property min_link

    ‘minimum linkage’ clustering used.

    This property controls the addition of the -min_link switch, treat this property as a boolean.

  property mot

    ‘motif’ option.

    This controls the addition of the -mot parameter and its associated value. Set this property to the argument value required.

  property msf

    Separate output file in MSF format.

    This property controls the addition of the -msf switch, treat this property as a boolean.

  property n

    Input sequences are nucleic acid sequences. No translation of fragments.

    This property controls the addition of the -n switch, treat this property as a boolean.

  property nt

    Input sequences are nucleic acid sequences and ‘nucleic acid segments’ are translated to ‘peptide segments’.

    This property controls the addition of the -nt switch, treat this property as a boolean.

  property nta

    ‘no textual alignment’ - textual alignment suppressed. This option makes sense if other output files are of interest – e.g. the fragment files created with -ff, -fop, -fsm or -lo.

    This property controls the addition of the -nta switch, treat this property as a boolean.

  property o

    Fast version, resulting alignments may be slightly different.

    This property controls the addition of the -o switch, treat this property as a boolean.

  property ow

    Overlap weights enforced (By default, overlap weights are used only if up to 35 sequences are aligned since calculating overlap weights is time consuming).

    This property controls the addition of the -ow switch, treat this property as a boolean.

  property pst

    ‘print status’. Creates and updates a file *.sta with information about the current status of the program run. This option is recommended if large data sets are aligned since it allows the user to estimate the remaining running time.

    This property controls the addition of the -pst switch, treat this property as a boolean.

  property smin

    Minimum similarity value for first residue pair (or codon pair) in fragments. Speeds up protein alignment or alignment of translated DNA fragments at the expense of sensitivity.

    This property controls the addition of the -smin switch, treat this property as a boolean.

  property stars

    Maximum number of ‘*’ characters indicating degree of local similarity among sequences. By default, no stars are used but numbers between 0 and 9, instead.

    This controls the addition of the -stars parameter and its associated value. Set this property to the argument value required.

  property stdo

    Results written to standard output.

    This property controls the addition of the -stdo switch, treat this property as a boolean.

  property ta

    Standard textual alignment printed (overrides suppression of textual alignments in special options, e.g. -lgs)

    This property controls the addition of the -ta switch, treat this property as a boolean.

  property thr

    Threshold T = x.

    This controls the addition of the -thr parameter and its associated value. Set this property to the argument value required.

  property xfr

    ‘exclude fragments’ - list of fragments can be specified that are NOT considered for pairwise alignment

    This property controls the addition of the -xfr switch, treat this property as a boolean.

class Bio.Align.Applications.ProbconsCommandline(cmd='probcons', **kwargs)

  Bases: `AbstractCommandline`

  Command line wrapper for the multiple alignment program PROBCONS.

  http://probcons.stanford.edu/

  Notes

  Last checked against version: 1.12

  References

  Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.

  Examples

  To align a FASTA file (unaligned.fasta) with the output in ClustalW format, and otherwise default settings, use:

      >>> from Bio.Align.Applications import ProbconsCommandline
      >>> probcons_cline = ProbconsCommandline(input="unaligned.fasta",
      ...                                      clustalw=True)
      >>> print(probcons_cline)
      probcons -clustalw unaligned.fasta

  You would typically run the command line with probcons_cline() or via the Python subprocess module, as described in the Biopython tutorial.

  Note that PROBCONS will write the alignment to stdout, which you may want to save to a file and then parse, e.g.:

      stdout, stderr = probcons_cline()
      with open("aligned.aln", "w") as handle:
          handle.write(stdout)
      from Bio import AlignIO
      align = AlignIO.read("aligned.fasta", "clustalw")

  Alternatively, to parse the output with AlignIO directly you can use StringIO to turn the string into a handle:

      stdout, stderr = probcons_cline()
      from io import StringIO
      from Bio import AlignIO
      align = AlignIO.read(StringIO(stdout), "clustalw")

  __init__(cmd='probcons', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 15
  __static_attributes__ = ('parameters',)
  property a

    Print sequences in alignment order rather than input order (default: off)

    This property controls the addition of the -a switch, treat this property as a boolean.

  property annot

    Write annotation for multiple alignment to FILENAME

    This controls the addition of the -annot parameter and its associated value. Set this property to the argument value required.

  property clustalw

    Use CLUSTALW output format instead of MFA

    This property controls the addition of the -clustalw switch, treat this property as a boolean.

  property consistency

    Use 0 <= REPS <= 5 (default: 2) passes of consistency transformation

    This controls the addition of the -c parameter and its associated value. Set this property to the argument value required.

  property emissions

    Also reestimate emission probabilities (default: off)

    This property controls the addition of the -e switch, treat this property as a boolean.

  property input

    Input file name. Must be multiple FASTA alignment (MFA) format

    This controls the addition of the input parameter and its associated value. Set this property to the argument value required.

  property ir

    Use 0 <= REPS <= 1000 (default: 100) passes of iterative-refinement

    This controls the addition of the -ir parameter and its associated value. Set this property to the argument value required.

  property pairs

    Generate all-pairs pairwise alignments

    This property controls the addition of the -pairs switch, treat this property as a boolean.

  property paramfile

    Read parameters from FILENAME

    This controls the addition of the -p parameter and its associated value. Set this property to the argument value required.

  property pre

    Use 0 <= REPS <= 20 (default: 0) rounds of pretraining

    This controls the addition of the -pre parameter and its associated value. Set this property to the argument value required.

  property train

    Compute EM transition probabilities, store in FILENAME (default: no training)

    This controls the addition of the -t parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report progress while aligning (default: off)

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property viterbi

    Use Viterbi algorithm to generate all pairs (automatically enables -pairs)

    This property controls the addition of the -viterbi switch, treat this property as a boolean.

class Bio.Align.Applications.TCoffeeCommandline(cmd='t_coffee', **kwargs)

  Bases: `AbstractCommandline`

  Commandline object for the TCoffee alignment program.

  http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html

  The T-Coffee command line tool has a lot of switches and options. This wrapper implements a VERY limited number of options - if you would like to help improve it please get in touch.

  Notes

  Last checked against: Version_6.92

  References

  T-Coffee: A novel method for multiple sequence alignments. Notredame, Higgins, Heringa, JMB,302(205-217) 2000

  Examples

  To align a FASTA file (unaligned.fasta) with the output in ClustalW format (file aligned.aln), and otherwise default settings, use:

      >>> from Bio.Align.Applications import TCoffeeCommandline
      >>> tcoffee_cline = TCoffeeCommandline(infile="unaligned.fasta",
      ...                                    output="clustalw",
      ...                                    outfile="aligned.aln")
      >>> print(tcoffee_cline)
      t_coffee -output clustalw -infile unaligned.fasta -outfile aligned.aln

  You would typically run the command line with tcoffee_cline() or via the Python subprocess module, as described in the Biopython tutorial.

  SEQ_TYPES = ['dna', 'protein', 'dna_protein']
  __init__(cmd='t_coffee', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 14
  __static_attributes__ = ('parameters',)
  property convert

    Specify you want to perform a file conversion

    This property controls the addition of the -convert switch, treat this property as a boolean.

  property gapext

    Indicates the penalty applied for extending a gap (negative integer)

    This controls the addition of the -gapext parameter and its associated value. Set this property to the argument value required.

  property gapopen

    Indicates the penalty applied for opening a gap (negative integer)

    This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

  property infile

    Specify the input file.

    This controls the addition of the -infile parameter and its associated value. Set this property to the argument value required.

  property matrix

    Specify the filename of the substitution matrix to use. Default: blosum62mt

    This controls the addition of the -matrix parameter and its associated value. Set this property to the argument value required.

  property mode

    Specifies a special mode: genome, quickaln, dali, 3dcoffee

    This controls the addition of the -mode parameter and its associated value. Set this property to the argument value required.

  property outfile

    Specify the output file. Default: <your sequences>.aln

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property outorder

    Specify the order of sequence to outputEither ‘input’, ‘aligned’ or <filename> of Fasta file with sequence order

    This controls the addition of the -outorder parameter and its associated value. Set this property to the argument value required.

  property output

    Specify the output type.

    > One (or more separated by a comma) of: ‘clustalw_aln’, ‘clustalw’, ‘gcg’, ‘msf_aln’, ‘pir_aln’, ‘fasta_aln’, ‘phylip’, ‘pir_seq’, ‘fasta_seq’

    This controls the addition of the -output parameter and its associated value. Set this property to the argument value required.

  property quiet

    Turn off log output

    This property controls the addition of the -quiet switch, treat this property as a boolean.

  property type

    Specify the type of sequence being aligned

    This controls the addition of the -type parameter and its associated value. Set this property to the argument value required.

class Bio.Align.Applications.MSAProbsCommandline(cmd='msaprobs', **kwargs)

  Bases: `AbstractCommandline`

  Command line wrapper for MSAProbs.

  http://msaprobs.sourceforge.net

  Notes

  Last checked against version: 0.9.7

  References

  Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: “MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities”. Bioinformatics, 2010, 26(16): 1958 -1964

  Examples

      >>> from Bio.Align.Applications import MSAProbsCommandline
      >>> in_file = "unaligned.fasta"
      >>> out_file = "aligned.cla"
      >>> cline = MSAProbsCommandline(infile=in_file, outfile=out_file, clustalw=True)
      >>> print(cline)
      msaprobs -o aligned.cla -clustalw unaligned.fasta

  You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial.

  __init__(cmd='msaprobs', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 15
  __static_attributes__ = ('parameters',)
  property alignment_order

    print sequences in alignment order rather than input order (default: off)

    This property controls the addition of the -a switch, treat this property as a boolean.

  property annot

    write annotation for multiple alignment to FILENAME

    This controls the addition of the -annot parameter and its associated value. Set this property to the argument value required.

  property clustalw

    use CLUSTALW output format instead of FASTA format

    This property controls the addition of the -clustalw switch, treat this property as a boolean.

  property consistency

    use 0 <= REPS <= 5 (default: 2) passes of consistency transformation

    This controls the addition of the -c parameter and its associated value. Set this property to the argument value required.

  property infile

    Multiple sequence input file

    This controls the addition of the infile parameter and its associated value. Set this property to the argument value required.

  property iterative_refinement

    use 0 <= REPS <= 1000 (default: 10) passes of iterative-refinement

    This controls the addition of the -ir parameter and its associated value. Set this property to the argument value required.

  property numthreads

    specify the number of threads used, and otherwise detect automatically

    This controls the addition of the -num_threads parameter and its associated value. Set this property to the argument value required.

  property outfile

    specify the output file name (STDOUT by default)

    This controls the addition of the -o parameter and its associated value. Set this property to the argument value required.

  property verbose

    report progress while aligning (default: off)

    This property controls the addition of the -v switch, treat this property as a boolean.

  property version

    print out version of MSAPROBS

    This controls the addition of the -version parameter and its associated value. Set this property to the argument value required.

Biopython v: 1.85

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